Briefly: Except for the fact the same Congress which ratified the First Amendment (which allegedly separates church and state) also hired chaplains, and except for the fact that this same Congress began with prayer, and except for the fact that they passed a resolution declaring a day of thanksgiving to God, and except for the fact that Article I, Section 7 of the U.S. Constitution specifically makes provision for Sunday as a day of rest, and except for the fact that military chaplains pre- and post-date the Constitution of the United States, and except for the fact that the Supreme Court itself opens with prayer, and except for many other such accepted instances of comingling of religion and government within our nation's history, one could probably make a pretty good case that the Founding Fathers wanted to divorce religion completely from government.
The problem with the separation of church and state extremists is that they have to turn a blind eye to these and other historical events and situations, or fumble about in vain trying to explain them away. The attempts of these revisionists to blur the common sense reality of our country's history are nothing if not amusing, but it's a shame that they have been so blinded by their extremist ideology.
When did this madness begin? Opinions vary. Some say it was with the
Supreme Court decision in Everson v. Board of Education. Others say it
was in the early '60s, when the Supreme Court handed down a ruling prohibiting
teacher-led non-denominational prayer in public schools (Engel v. Vitale).
Others claim to trace it back to Thomas Jefferson. The positions could
be argued in various ways, but I think it began with Engel v. Vitale, as
that is where the extremist rubber really met the road. In this decision,
the Supreme Court ruled that teachers in public schools (or any school
officials) may not lead students in the following prayer:
Hardly the stuff of controversies, but the Supreme Court, ignoring sound principles of First Amendment jurisprudence, ruled that it was unconstitutional.
This kind of extremism has snowballed for the last thirty or so years,
until it has reached a kind of madness which we'll see in the next section.
It is this radical "kick God out of everything that has anything to do
with the government" mentality that is opposed here.
 See Engel